1 1C genome size and n chromosome number for bryophytes.2 Position refers to that of most chromosomes in the species and can be either interstitial (i), (peri-)centromeric (c) and (sub-)terminal or satellite (t).3 35S=45S=18S-5.8S-26S rDNA

New applications and improvements

New information on sequenced plant genomesNEW

Information on plant species whose genome has been fully sequenced. The page allows browsing publications of plant genomes sequenced by family. Every species is linked with the corresponding publication presenting the sequenced genome.

New information on telomere composition NEW

Data on telomere motives has been extracted from the same source publication of rDNA-FISH in the cases where this information was included. Additionally, other general sources on telomere composition have been used. Some assumptions have been made to organize the data. When a given telomere sequence was confirmed for several species in a genus, this has been considered that any other species from the same genus would present the same telomere sequence. We also state that a given species may have “probably” or “possibly” a given telomere type when there is evidence at the family or order level, respectively. Where there is no evidence above the taxonomic level order the status is “unknown”. In few cases (particularly in species of order Asparagales) presence of more than one telomere signal may be due cross-hybridisation between telomere probes.

Visual 2C (Genome size representation tool)

If genome size data is available for a given species it appears represented as a blue bar whose size is directly proportional to 2C value. A red line in the graph will indicate the mean genome size for the genus to which the species belongs. This provides a comparison between genome sizes of related species at a glance. See an example here:

NOR

In this new section we provide information about the transcriptional activity of the 35S loci, checking the presence of secondary constrictions, satellites or NORs (nucleolar organiser regions, the hallmarks of transcription activity of residing rRNA genes) whenever the publication stated this, i.e. if experiments based on silver nitrate staining had been done, or when the satellites or secondary constrictions were evident in the chromosome spreads. Therefore, an “x” mark in the NOR box indicates that the paper contains evidence of transcriptional activity, but it does not state how many rDNA loci are actually active.

K (Karyotype tool)

This application offers a visual representation of the karyotypes from the data provided in the database, without the need of consulting the source application. The karyotype will appear in a pop-up window when clicking the chromosome symbol in the K box. These are the basic chromosome types:

All the other possible chromosome types and signal combinations can be consulted here.

NOTES

Due to the complexity of translating data into pictures, some premises and assumptions have been considered to simplify the application:

Since the database does not include information on chromosome morphology at this stage, all chromosomes are depicted as metacentric, with the exception of holocentric chromosomes.

In few cases (like in genera Alstroemeria, Iris, Pinus or Tulipa, and few scattered species) there are several chromosomes with more than one rDNA signal of the same type (5S and 35S). The database does not yet include this information, so karyotypes of these taxa will not be shown to avoid data misinterpretation.

As explained below, in some species there may be more than one possible location for a given rDNA signal. When it is stated that signals are found in two different locations, the karyotype will show half of the chromosomes marked in one location, and the other half in the other (i. e. if there are six 35S interstitial – telomeric signals, the graphic will display three chromosomes with interstitial 35S and three more with telomeric 35S). The same rule is followed when the signals are found in three locations.

In some cases, the number of chromosomes with signals located in different positions might be odd. In these cases the program substracts 1 and divides the remaining number into the two or three positions. The one left is added to the first group of positions which is the most frequently found if any.

Exceptionally, we have used the terms “some” or “several” when the number of signals was not determined by the source publication and was impossible to ascertain. We make the assumption that “some” means 20% of chromosomes with signals, while “several” will mean 50% of chromosomes with signals.

Occasionally, the chromosome number is unknown. Only the chromosomes bearing rDNA loci will be depicted in the karyotypes in these exceptions.

Help with searching

The plantrDNAdatabase has been organized so that you can make either a Simple or an Advanced Search.

Simple Search

The Simple Search is basic and aimed to obtain easily fast results. You only have to type the name of the family, genus, species or even specific epithet of your interest in the Search Box and the results will automatically be displayed.

By default, the information that will appear in this type of search, besides chromosome number and ploidy level, is: number and position of 5S and 35S signals, presence of a linked 5S-35S arrangement and ID number of the source publication (Ref.) whose complete name will appear by moving your cursor over it. You can also obtain, by clicking the options below the search box, the authority of the plant name and the 2C genome size (in pg). The total number of records for your search is shown at the right top of the results. A given Simple Search can be later refined by clicking in the Advanced Search and selecting any of the available options.

NOTE: With some of the type genera of families, those that have left their complete name for the name of the family, when typing their names, information on data of the full family will appear. This will only happen in these cases:

Aster (Asteraceae)

Brassica (Brassicaceae)

Carica (Caricaceae)

Cucurbita (Cucurbitaceae)

Musa (Musaceae)

Rosa (Rosaceae)

Zamia (Zamiaceae)

This can be avoided by clicking once the space bar after the name of the genus.

Advanced Search

The Advanced Search allows different options to refine your search. You can access from any tab of the webpage (excepting ‘News’) by clicking the word ‘Advanced’ highlighted in bold. Then a query form will appear.

In the first section of the query form you can select, by clicking in the corresponding box, all the output fields that you want in your search record. There are some options ticked by default (explained at the Simple Search).

Therefore, if you want additional information, like life cycle or number of chromosomes with co-localized 5S and 35S signals, for example, then click in the appropriate boxes and these data will be shown if available:

The second section allows you writing conditions, where it can be chosen that only results for a given family, genus or species are shown. Also, you can choose that your search only presents results for (a) given ploidy level(s) and chromosome number(s).

For example, you can ask the database to give you rDNA data for diploid to tetraploid Brassicaceae by entering ‘Brassicaceae’ in the family box and entering ‘2’ and ‘4’ in the ploidy level boxes:

NOTE: Numbers have to be written in arabic numerals.

Finally, the third section enables to apply filters to your search either by land plant group, division, angiosperm group (of course only applicable to angiosperms) and life cycle (see figure below). There is a last option that permits to sort the results by family, genus, species, genome size, chromosome number or ploidy level; as for the previous filters, the appropriate choice has to be selected from the drop-down box under the option 'Sort by' at the bottom of the query form. The results of searches are automatically sorted by alphabetical order.

Once the different options are chosen, click the ‘Search’ button at the right bottom of the query form. To perform subsequent advanced searches you can refresh the query form by clicking the ‘Delete’ button at the right top of the form.

NOTES:

FAMILY NOMENCLATURE

The standard/APG (Angiosperm Phylogeny Group) family names have been followed in the webpage, even in the cases that the original publications used the traditional, non-standard family names. Also there are some recent phylogenetic changes that have been considered, which merge some families into others. Here you will find a correspondence:

POSITION OF SIGNALS IN CHROMOSOMES

The positions of rDNA signals in chromosomes have been reduced to only three different options for the sake of clarity. These are:

Centromeric or pericentromeric (if they are close to the centromeres)

Interstitial (meaning positions near to the middle part of the chromatids)

Telomeric or subtelomeric (if they are close to the telomeres)

Satellite

Only the most abundant position has been selected to characterize each kind of rDNA loci, although in some species there may be more than one possible location. The source publication should always be consulted in case of doubt.

Once the Advanced Search is started, you cannot use the Simple Search unless you refresh your query form (by clicking the button ‘Delete’) or your session.